Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Availability and Restrictions

The following versions of Bowtie2 are available on OSC clusters:

Version Oakley Owens
2.2.8 X*  
2.2.9   X*
*: Current default version

You can use  module spider bowtie2  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Bowtie2 is available to all OSC users without restriction.

Usage on Oakley

Set-up

To configure your environment for use of Bowtie2, run the following command:   module load bowtie2  . The default version will be loaded. To select a particular Bowtie2 version, use   module load bowtie2/version . For example, use  module load bowtie2/2.2.8  to load Bowtie2 2.2.8.

Usage on Owens

Set-up

To configure your environment for use of Bowtie2, run the following command:    module load bowtie2  . The default version will be loaded. To select a particular Bowtie2 version, use    module load bowtie2/version . For example, use  module load bowtie2/2.2.9  to load Bowtie2 2.2.9.

Further Reading

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